Research workbench
Structure of chicken acid-sensing ion channel 1 at 3.0 a resolution in complex with psalmotoxin
Analyse Structure of chicken acid-sensing ion channel 1 at 3.0 a resolution in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S3X
- Type
- protein
- Length
- 1,299 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amiloride-sensitive cation channel 2, neuronal; Psalmotoxin-1
- UniProt
- Q1XA76, P60514
- Ligands
- NAG, K, CL, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amiloride-sensitive cation channel 2, neuronal | protein | 401 | 31% helix, 25% strand | Q1XA76 |
| B | Amiloride-sensitive cation channel 2, neuronal | protein | 391 | 29% helix, 27% strand | Q1XA76 |
| C | Amiloride-sensitive cation channel 2, neuronal | protein | 396 | 33% helix, 26% strand | Q1XA76 |
| D, E, F | Psalmotoxin-1 | protein | 37 | 0% helix, 30% strand | P60514 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- K · Potassium ion · metal · 2 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, C
- SO4 · Sulfate ion · ion · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.82 | 0.95 | 30 | empty |
| 2 | 585 | 0.80 | 0.86 | 88 | K |
| 3 | 290 | 0.80 | 0.92 | 38 | K |
| 4 | 445 | 0.80 | 0.88 | 58 | empty |
| 5 | 430 | 0.79 | 0.87 | 59 | empty |
Interfaces
9 interfaces between chains.
- A–C · 2419 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2048 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2031 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 759 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 752 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3S3X · Structure of chicken acid-sensing ion channel 1 AT 3.0 A resolution in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q1XA76 · AlphaFold monomer V2.0 prediction for acid-sensing ion channel 1 (Q1XA76) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P60514 · AlphaFold monomer V2.0 prediction for psalmotoxin-1 (P60514) · a predicted model of the same protein · chain D against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q1XA76
- Every structure of UniProt P60514
- Elsewhere: RCSB PDB 3S3X · PDBe 3S3X · UniProt Q1XA76 · UniProt P60514
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